EMD-8481

Single-particle
3.9 Å
EMD-8481
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Deposition: 28/11/2016
Map released: 11/01/2017
Last modified: 13/03/2024
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EMD-8481
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Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
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EMICSS annotations (xml)

Structure of tetrameric HIV-1 Strand Transfer Complex Intasome

EMD-8481

Single-particle
3.9 Å
EMD-8481
3D View Gallery
Deposition: 28/11/2016
Map released: 11/01/2017
Last modified: 13/03/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 0.5 mg/mL
Buffer
pH: 8.0
Buffer components [4]:
Name Formula Concentration ChEBI
Sodium chloride NaCl 500.0 mg/mL
Tris C4H11NO3 20.0 mM
TCEP C9H15O6P 0.5 mM
Glycerol C3H8O3 6.0 %
Grid
Mesh: 400
Model: Quantifoil
Material: GOLD
Pretreatment
Type: PLASMA CLEANING
Time: {'units': 's', 'valueOf_': '6'}
Atmosphere: OTHER
Vitrification
Cryogen name: ETHANE
Chamber humidity: 50%
Chamber temperature: 277 K
Instrument: HOMEMADE PLUNGER
Details: Sample containing HIV STC intasomes in SEC buffer was applied onto freshly plasma-treated (6 seconds, Gatan Solarus plasma cleaner) holey gold UltrAuFoil grids (Quantifoil), adsorbed for 30 seconds, then plunged into liquid ethane using a manual cryo-plunger in an ambient environment of 4 degrees C..
Microscopy [1]
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
C2 aperture diameter: 100.0 µm
Nominal CS: 2.7 mm
Calibrated defocus: 1.5 µm - 4.0 µm
Nominal magnification: 22500.0
Calibrated magnification: 38167.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Temperature
Minimum: 90.0 K
Maximum: 90.0 K
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: COUNTING
Dimensions: 3838 pixel x 3710 pixel
Frames per image: 1-100
Number of grids: 1
Number of real images: 1225
Average exposure time: 20.0 s
Average electron dose per image: 95.0 e/Å2
Details: Individual frames were gain-corrected, aligned, and summed with the application of an exposure filter using MotionCor2, according to the nominal dose rate.
Image processing [1]
Final reconstruction
Resolution: 3.9 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of images used: 83766
Algorithm: FOURIER SPACE
⌯ Applied Symmetry
Point group: C2
Software [1]
Name Version Details
FREALIGN 9.11 -
Startup model [1]
Type: INSILICO MODEL
Insilico model: Common lines model using OptiMod
Details:An initial model was generated directly from the class averages using OptiMod.
⦨ Initial angle assignment
Type: PROJECTION MATCHING
Angular sampling: 7.5 degrees
Details: Relion 3D classification, auto mode
Software [1]
Name Version Details
RELION 1.3 -
⦩ Final angle assignment
Type: PROJECTION MATCHING
Details: Frealign 3D classification and refinement
Software [1]
Name Version Details
FREALIGN 9.11 -
Particle selection [1]
Selected Ref. model Method Software Details
274764 - - - -
Final 3D classification
Software [1]
Name Version Details
FREALIGN 3.11 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: CryoEM reconstruction of a tetrameric HIV-1 strand transfer complex intasome
⬡ Geometry
X Y Z
Dimensions 192 192 192
Origin 0 0 0
Spacing 192 192 192
Voxel size 1.31 Å 1.31 Å 1.31 Å
Contour list
Primary Level Source
True 0.08 AUTHOR